Variant report

Variant	rs8003056
Chromosome Location	chr14:38991928-38991929
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11849364	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12881405	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12889522	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17108119	0.99[EUR][1000 genomes]
rs28822206	0.83[AMR][1000 genomes]
rs34786299	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34841603	0.96[EUR][1000 genomes]
rs35374049	0.98[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4463992	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs5018011	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73284631	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8008331	0.96[AMR][1000 genomes]
rs8009592	0.96[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533235	chr14:38558180-39117391	Weak transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv901655	chr14:38887881-39019800	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
3	nsv564410	chr14:38944821-39038281	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
4	nsv1037223	chr14:38950249-39044313	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
5	nsv1038162	chr14:38950615-39033944	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
6	nsv1051236	chr14:38952989-39039159	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
7	nsv1051499	chr14:38952989-39044313	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
8	nsv564411	chr14:38958967-39025057	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
9	nsv564412	chr14:38958967-39025120	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
10	nsv515869	chr14:38958967-39038281	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
11	nsv456211	chr14:38958967-39038281	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
12	nsv564413	chr14:38958967-39038281	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
13	nsv564414	chr14:38958967-39058922	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
14	nsv564415	chr14:38958967-39075178	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs8003056	TRAPPC6B	cis	parietal	SCAN
rs8003056	NKX2-1	cis	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:38982600-38992000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr14:38991800-38992000	Enhancers	iPS-18 Cell Line	embryonic stem cell
3	chr14:38991800-38992400	Enhancers	Muscle Satellite Cultured Cells	--
4	chr14:38991800-38992600	Enhancers	HUES48 Cell Line	embryonic stem cell
5	chr14:38991800-38993400	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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